Life – K from a nice volcanic mud puddle…

I’ve complained a few times in a few places about one of the Nagging Bits about cellular function that just doesn’t fit with the idea we evolved in the ocean on earth.

That is the fact that cells contain a LOT of K Potassium, and less Na Sodium, while the ocean has a lot of Na and not so much K.

“If we evolved in the ocean, why do our cells have pumps to keep the sodium out?”

I’d speculated that this could be evidence for panspermia, that maybe life originally evolved in some other cosmic ocean and got carried here. I’ve speculated it could even indicate Divine Intervention was useful in the getting started phase.

Then a comment on a WUWT article pointed me toward a Very Interesting Paper that has a tidy way of tying up the loose ends.

http://www.pnas.org/content/109/14/E821

Origin of first cells at terrestrial, anoxic geothermal fields

Armen Y. Mulkidjaniana,b,1, Andrew Yu. Bychkovc, Daria V. Dibrovaa,d, Michael Y. Galperine, and Eugene V. Koonine,1

Author Affiliations

Edited* by Norman H. Sleep, Stanford University, Stanford, CA, and approved January 17, 2012 (received for review October 28, 2011)

Abstract

All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the “hatcheries” of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate. Thus, protocells must have evolved in habitats with a high K+/Na+ ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO2-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K+, Zn2+, and phosphorous compounds.

There are some papers that just reek of unjustified leaps, or “given these conclusions what assumptions can we draw?”, or some are just sort of muddied untidy things. This paper is not one of them.

There are other papers that are somehow “just right”. Loose threads at the start, neatly tied off by the end. Things you’d not thought of, brought up and examined. A basic idea that expands what it explains with each paragraph, rather than creating more “issues” as you read. This is that kind of paper.

Not just K/Na ratio, but the excess phosphate, the large use of Zn in enzymes, and so much more. Neatly tied up in a self consistent and very reasonable package.

The full PDF is here: http://www.pnas.org/content/109/14/E821.full.pdf

Essentially, the authors looked at those same issues (like K/Na ratios and ion pumps), but also thought about why they would form, how life could evolve slowly bit by bit and only later add things like ion-tight membranes and ion pumps, how geology could make those conditions, and where. Then they connect all those dots into one nice picture.

Hit the link, read the PDF, bits quoted can’t do it justice.

But a couple of bits:

Origin of first cells at terrestrial, anoxic geothermal fields

Armen Y. Mulkidjanian a,b,1, Andrew Yu. Bychkov c, Daria V. Dibrova a,d, Michael Y. Galperin e, and Eugene V. Koonin e,1

a School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany;
b A. N. Belozersky Institute of Physico-Chemical Biology and Schools of
c Geology and
d Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia; and
e National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

Edited* by Norman H. Sleep, Stanford University, Stanford, CA, and approved January 17, 2012 (received for review October 28, 2011)
[…]

For example, ancient, ubiquitous proteins often use Zn and Mn, but not Fe, as transition metal cofactors; this preference is retained across the three domains of life (12). The abundance of Zn- and Mn-dependent enzymes during the earliest steps of evolution and the later recruitment of Fe has been inferred also from a global phylogenomic re-construction (13). The prevalence of Zn-dependent ancestral enzymes is particularly remarkable given the low estimated concentration of Zn in the anoxic ocean of 10^−12 to 10^−16 M (14,15) and indicates that the first organisms might have dwelled inspecific, Zn-enriched habitats (12, 16). Here we combine geochemical evidence with the data on the overall ionic composition of the modern cells, with a particular emphasis on their universal preference for K+ ions over Na+ ions. Geochemical analysis shows that, contrary to the common belief that associates the origin of life with marine environments, the first cells could have emerged at inland geothermal fields within ponds of condensed and cooled geothermal vapor.
[…]

It goes on from there. Showing why ocean origin can’t work (some enzymes that are essential can’t form or function with that much Na) and then on to look at geothermal fields, how they sort and stratify minerals, how with an atmosphere missing oxygen, they would make amines and even oils and RNA. Every thread that needs pulling gets pulled, and explained.

I was particularly fond of this bit, not for the origin of life angle, but for how nicely they cover formation of hydrocarbons. Life runs on oil. Cell membranes are lipid layers. So perhaps this also explains some of how abiotic oil can form? Bold mine.

The absence of any enzymes related to autotrophy in the ubiquitous protein set (SI Appendix, Table S1) suggests that the protocells were heterotrophs, i.e., their growth depended on the supply of abiotically produced organic compounds (32, 75–77). At least two continuous, abiotic sources of such compounds would exist in the described geothermal systems. First, even in modern vapor-dominated geothermal systems, exhalations carry organic molecules that are believed to be formed, at least partly, in the process of hydrothermal alteration of ultramafic rocks (78,79). Hydrothermal alteration occurs when iron-containing rocks interact with water at temperatures of approximately 300 °C, which is typical of terrestrial geothermal systems. Under these conditions, part of the Fe 2+ in the rock is oxidized to Fe3+, yielding magnetite (Fe3O4). The electrons released through this reaction are accepted by protons of water yielding H2; in the presence of water-dissolved CO2, diverse hydrocarbons are ultimately produced (78). It could be argued that the hydrothermal rock alteration might also account for the reduction of insoluble apatite to soluble phosphite (47), explaining the presence of phosphite in the geothermal fluids (56). Similar reactions couldlead to the ammonia formation (80), which might account for the high ammonia content in the exhalations of geothermal fields [as much as 130 mg/L in the mud pot solutions of Kamchatka (55)]. In addition, diverse organic molecules could be produced by abiotic photosynthesis catalyzed by ZnS and MnS particles (81–84). Such crystals are semiconductors, which can trap quanta with a λ of less than 320 nm and transiently store their energy in a form of charge-separated states, capable of reducing diverse compounds at the surface (81). Thereby, crystals of ZnS are the most powerful photocatalysts known in nature (10).‡ Particles of ZnS can catalyze photopolymerization reactions (85) and photo reduce carbonaceous compounds to diverse organic molecules, including intermediates of the tricarboxylic acid cycle (83, 84); the highest quantum yield of 80% was observed upon reduction of CO2 to formate (81).

So the paper is kind of a ‘two fer’. Pointers on abiotic oil and hydrocarbons, and an answer to why life is like it is. I’d only add that the general thought process most folks use, starts with our present cellular life and asks “How can this evolve all at once?”. Suddenly getting both RNA and DNA replication going and getting needed machinery like membrane ion pumps to evolve and install to let it all run. This paper solves some of the chemical issues.

My idea is that in such a puddle of chemicals, the whole puddle can be one living thing, only later dividing up into cells with control of ions at the membrane. Look at some of the slime molds. They can break up or not, and have many different nuclear areas inside one giant ‘cell’. I’d envision a large puddle of RNA, hydrocarbons (fats) and such. Slowly making RNA replicators and very leaky membranes (since the environment is essentially making cytoplasm, you don’t really want to keep it out). Only later breaking up into droplets with “cell walls” and adding ion pumps over a very long period of time. As those lumps with better internal control replicate more and die off less in the rain (or a seawater splash…)

This lets many bits of interior mechanism develop over a very long time ( RNA replication, fat metabolism, Citric Acid Cycle) only later working out how to make a nucleus and cell walls, and finally adding ion pumps to less leaky cell walls. At that point, cellular life as we know it can take over the world….

If the entire pond is the first life, then evolving bits slowly, and gradually approaching “final assembly” is much easier to have happen. The only hard bit is having that puddle make those bits. This article explains how that happens.

I’m pretty sure that those two things in conjunction explains how life can start.

For folks of a creationist bent: My standard way to resolve that with “Science” is simply to ask a question: Could this not be the method by which God created life? I see the study of chemistry, physics, biology, etc. as the study of the methods of the universe, and religion as the study of the meaning. Knowing the methods used does not change the meaning of creation… and personally I find the idea of creating a chemical system that self assembles into life a far more interesting act of creation. When I go looking for a file on my computer, I don’t open each file by hand; I write a bit of instructions to do the looking automatically. I’d expect a creator God to have at least that good a programming skill too… and I find the idea of me putting limits on how a God can work to be a bit cheeky.

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